Research in artificial complexity (i.e., artificial life, complex systems, and agent-based distillation), largely depends on the use of computer software. The reliability of the obtained results is directly related to two key assumptions: (1) that the software represents the problem as intended by the developer; and (2) that the software is bug-free. However, developing software for artificial complexity offers new challenges to software engineering, and it becomes imperative to discuss the software engineering problems arising in artificial complexity that are different from traditional computer programming. The first aim of this paper is to identify the possible challenges confronted by developers of systems involving artificial complexity. The second is to offer preliminary suggestions on how to incorporate existing software engineering techniques into artificial complexity's simulation development.